Freesurfer

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30132 discussions

fspalm error
by Barbour, Tracy,M.D. 09 Sep '19

09 Sep '19

Hello Freesurfer community! I am trying to run fspalm on surface based data. I have installed PALM, fspalm, mri_surfcluster, and mri_volcluster. This is my fspalm command: fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 --iters 1000 --2spaces --cwp .05 When I run the fspalm command I get the error: "for surface based analysis, input cannot be nii or nii.gz" I thought that fspalm was supposed to convert ces.nii.gz files into something that PALM could use. Please let me know if there is another step I need to run or if I need to change the script. Best, Tracy

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Re: [Freesurfer] Morphological Features, Description & References
by Loske, Philipp 09 Sep '19

09 Sep '19

External Email - Use Caution Hi you two, thank you very much for your quick reply! Just two short followup questions: @Bruce: Is this published in any paper or documentation so I can cite it? @Doug: Has this method been implemented with the last release of FS in 6.0.0 or already before in 5.3.0 (I'm still using this version)? Cheers Philipp For cortical volume we compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script. On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray/white boundary) surface. We also have some discrete measures of curvature that uses the Gauss-Bonnet theorem, but those aren't run by default. cheers Bruce On Fri, 6 Sep 2019, Loske, Philipp wrote: External Email - Use Caution Hello FreeSurfer Developers, I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values. I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search. Best wishes Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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error while running "-hippocampal-subfields-T1" with Freesurfer 6.0
by shahrzad kharabian 09 Sep '19

09 Sep '19

External Email - Use Caution Hi, I have already run recon-all with default options on a large set of T1-weighted images, using Freesurfer v 6.0. Now we want to extract the hippocmpal subfields from these already processed images. Apparently our installation was missing Matlab Compiler Runtime (MCR) for Matlab 2012b.We followed the instructions and downloaded it and placed it in the $FREESURFER_HOME. Yet now when running the "recon-all -s subj_id -hippocampal-subfields-T1" command, I get the following error: $FREESURFER_HOME/bin: Permission denied. and the error occurs in the step: $FREESURFER_HOME/bin/segmentSF_T1.sh --- I am using a bash shell. But also temporarily changing the shell to tcsh and adding the Freesurfer to the path, did not solve the problem. How can the error be avoided? Thanks a lot for your help in advance, Shahrazd

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multiple T2s
by Aaron Tanenbaum 08 Sep '19

08 Sep '19

External Email - Use Caution Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If so how does one get it to work. It only seems to use the last T2 in the call to recon-all.

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Re: [Freesurfer] mris_decimate error
by fsbuild 06 Sep '19

06 Sep '19

External Email - Use Caution Hello, On the Mac, we use homebrew to provide some libraries that freesurfer binaries need to link against in order to run, see https://brew.sh/ Once you install homebrew you should have a “brew” command available in the terminal window.  Then to get libglib you could try from the terminal, $ brew install glib … though it may tell you it is already installed.  You could also check that it exists with, $ ls /usr/local/lib/libglib-2..0.0.dylib/usr/local/lib/libglib-2.0.0.dylib@- R. On Sep 6, 2019, at 14:17, rockj5(a)netzero.net wrote:       External Email - Use Caution        When running mris_decimate on macOS High Sierra, I get this error:dyld: Library not loaded: /usr/local/lib/libglib-2.0.0.dylib Referenced from: /Applications/freesurfer/bin/mris_decimate Reason: image not foundAbort trap: 6Is this a library that was supposed to be installed by FreeSurfer? I did not make any changes to the installation so I am not sure why this error is occurring.Thanks to anyone that can help. I really appreciate it._______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_decimate error
by rockj5＠netzero.net 06 Sep '19

06 Sep '19

External Email - Use Caution When running mris_decimate on macOS High Sierra, I get this error: dyld: Library not loaded: /usr/local/lib/libglib-2.0.0.dylib Referenced from: /Applications/freesurfer/bin/mris_decimate Reason: image not found Abort trap: 6 Is this a library that was supposed to be installed by FreeSurfer? I did not make any changes to the installation so I am not sure why this error is occurring. Thanks to anyone that can help. I really appreciate it. ____________________________________________________________ $4.95 Natural Painkiller Working "Better Than Oxy" worldhealthlabs.com http://thirdpartyoffers.netzero.net/TGL3231/5d72a2fdd8cab22fd34fbst03duc

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Postdoc positions in cognitive and computational neuroscience
by Ivan Alekseichuk 06 Sep '19

06 Sep '19

External Email - Use Caution Multiple postdoc positions in cognitive neuroscience and computational neuroscience are available in the Opitz Lab, University of Minnesota! The lab works in the field of brain stimulation (with the focus on the transcranial methods – TMS, tACS/tDCS) across multiple levels of investigation. We conduct both computational research (using resources of Minnesota Supercomputing Institute) and human experimental research (EEG, ECoG, functional and structural MRI, psychophysics). In collaboration with other labs at the University of Minnesota, we perform basic research in animal models. Through the direct vicinity to the Medical School and Center for Magnetic Resonance Research, we have several collaborators who study brain stimulation in clinical populations. We are looking for a postdoc to contribute to our ongoing projects: closed-loop TMS-EEG, multiscale modeling of TMS/tACS, human research in neurophysiology of TMS/tACS, cognitive effects of brain stimulation in healthy humans and patients; or develop their own research agendas. Interest and ability to integrate into a multidisciplinary team is essential. The ideal candidate should have Ph.D. in applied quantitative field (Engineering, Physics, or Applied Mathematics) or life sciences (Neuroscience, Human Biology, or Cognitive Science). Strong technical and computational skills are preferred, but candidates with strong human experimental background are also encouraged to apply. The Opitz lab is committed to the career advancement of its members. We offer a diverse and inclusive environment with numerous opportunities for members to develop their own projects and support for fellowships and career development awards. Informal inquiries can be made to: aopitz(a)umn.edu See more on the website: http://opitzlab.umn.edu/join_us

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Re: [Freesurfer] Interruption during data processing
by Троицкий Антон Александрович 06 Sep '19

06 Sep '19

External Email - Use Caution Bruce, could you explain how can I do that? I mean what command should I use and parameters? Best regards, Anton Troitskii

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Question about how to build .gca files from non-human atlas and images
by arsene ella 06 Sep '19

06 Sep '19

External Email - Use Caution *Dear **Freesurfer experts,* *I’ve built an atlas of structures of a non-human average brain and now **I would like to build **its** .gca files from scratch. **From the Freesurfer mailing list, I saw that this is possible using **rebuild_gca_atlas.csh* *which trains labelled brai**ns (**seg_edited.mgz**) and their intensity volumes (it is said to use the **norm.mgz** for this purpose) from several subjects through **mri_ca_train**. **My questions are :**1) How to normalize my native intensity volume to a **norm.mgz** volume without .gca and .lta files asking by **mri_ca_normalize **?**Y**ou’ve suggested to give **mri_ca_normalize** a flag to tell it to use a manual segmentation instead of the gca by trying **-seg <manual seg volume>**. Then the gca name won't matter - it should ignore it… I tried this as followed :**let : **- **Brain_Template_T1_MPR.mgz ** be my intensity native volume**- **Brain_Cortex_Atlas.mgz* * be my manual segmented volume**- **Brain_Template_T1_MPR_norm.mgz* * be **my **norm** output** volume* *Command lines :**mri_ca_normalize** Brain_Template_T1_MPR.mgz **-seg** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR_norm.mgz**gave the following error message :**reading 1 input volume**reading atlas from '-seg'...**GCAread(-seg): could not open file**No such file or directory**mri_ca_normalize: could not open GCA -seg.**No such file or directory* *mri_ca_normalize* *-seg ** Brain_Cortex_Atlas.mgz Brain_Template_T1_MPR.mgz Brain_Template_T1_MPR_norm.mgz**gave the following message and stopped:**using segmentation volume /home/arsene/Bureau/FS_GCA/FS_SHEEP_CGA/Brain_Cortex_Atlas.mgz to generate control points...**usage: mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...* *What is wrong with theses **mri_ca_normalize* *commands ?* *2) My second question is to know how to transfert labels from my* *manual seg**mented** volume **(ex : **atlas.mgz**) to each single image volume (ex : vol1**.mgz**) ?**You’ve suggested to use **mri_label2label**, but **I didn’t see anything allowing me to do a **volume_to_volume** transfert **from **its **–help**…** If I got it wrong, could you suggest a command ?* *cheers* *Arsene*

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Morphological Features, Description & References
by Loske, Philipp 06 Sep '19

06 Sep '19

External Email - Use Caution Hello FreeSurfer Developers, I have a question about references and descriptions to all the morphological features available in aparc.stats, extracted from structural MRI. I am using all the different features (SurfArea, GrayVol, ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd, CurvInd) for the 68 cortical regions available from the Desikan Kiliany atlas. I have been trying to find references to how these features are measured or derived, but couldn't find a proper list of references to each of the features. I a lot of references here https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation, with detailed descriptions on surface reconstruction and how cortical thickness is measured, but couldn't find a detailed explanation on the other features, especially curvature values. I think I have been able to find out what each of the measurements mean and how they are calculated in principle, through searching the internet a lot, but with no direct link to FreeSurfer. For instance, I know you can calculate the curvature values from the principle curvatures, but how does FS estimate those form the reconstructed Surface? And which one of the two surfaces does it use? White-pial or pial-csf surface? I found https://brainder.org/ really helpful, but it says for example that a new way of measuring cortical volume was implemented in FS 6.0.0, so does that mean for previous versions FS uses the Thickness x SurfaceArea method? Would be great if you can help me with this, or point me to the correct website I might just have missed during my search. Best wishes Philipp The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas clàraichte ann an Alba, Àir. SC013683.

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